

Near optimal alignment generation
Version:  rel-2-1
2004/06/14 19:10:24
=================================

This software is written in C++ and uses the standard GNU Autoconf tools
for installation, meaning the software should install without much
difficulty on any Unix variant (Linux, OS X, etc.).  Presumably this will 
work on Windows as well, perhaps with Ming or Cygwin, but we have no 
experience on those platforms.

These instructions assume that you will install the software in a standard
location.  If you need to install the software in a non-standard location,
please read the INSTALL file included with either package for details.


TCLAP Installation
------------------

First install the TCLAP package.  This is available at 
http://tclap.sourceforge.net.  Simply unpack the tar file:

	% tar -xvzf tclap-X.X.tar.gz

Then configure and make: 
	
	% cd tclap-X.X
	% ./configure
	% make
	% make check

Assuming the tests run correctly, then install, either as root or using sudo:

	% sudo make install


noptalign installation
----------------------

Once tclap is installed, then install noptalign.  The procedure is 
identical to that of tclap:

	% tar -xvzf noptalign-rel-X-X.tar.gz
	% cd nopalign-rel-X-X
	% ./configure
	% make
	% make check
	% sudo make install


Noptalign should now be installed. Two programs (noptalign, scorealign) and 
their associated man pages, libraries, etc. should be installed.  noptalign
is the primary program of interest and generates the near optimal alignments. 
scorealign is a simple utility used for scoring alignments generated using
other algorithms. Simply type:
	
	% noptalign

for a help message.  There is also a man page that provides slightly more
detail.  Here is an example invocation:

	% noptalign -1 seq1.fasta -2 seq1.fasta -f -11 -g -1 -s BLOSUM62 -b 0.98

which will use BLOSUM62 -11/-1 to align seq1 and seq2 with a neighborhood of
98% of optimal.


